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United States Department of Agriculture

Agricultural Research Service


Location: Hard Winter Wheat Genetics Research Unit

2011 Annual Report

1a.Objectives (from AD-416)
Objective 1: Develop adapted hard red or white wheat germplasm lines with improved resistance to emerging or intractable problems in wheat production and marketing.

Objective 2: Increase understanding of the molecular basis of parasite virulence, host resistance, and stress tolerance for these problems.

Objective 3: Develop and apply phenotypic and genotypic selection technology for these traits to hard red or white winter wheat germplasm or cultivar development.

1b.Approach (from AD-416)
Production of high quality hard red or white winter wheat is limited by recurring intractable problems such as leaf rust, Fusarium head blight, Hessian fly, and heat stress during the grain filling period. In addition, new emerging problems such as stripe rust, stem rust, and Karnal bunt threaten the production or marketing of high quality grain. The first objective of this project is to develop adapted hard red or white wheat germplasm lines with improved resistance or tolerance to these problems. We will utilize existing sources and identify new sources of resistance, introgress them into desirable backgrounds, and then release them for use as parents of commercial cultivars. The second objective is to increase our understanding of the molecular basis of parasite virulence, host resistance, and stress tolerance to support strategic development and deployment of genetic resistance. Greater understanding of secreted virulence/avirulence effectors in the Hessian fly and the leaf rust pathogen may lead to better strategies for durability. Greater understanding of the mechanisms of durable rust resistance and heat tolerance may lead to discovery of new genes or alleles with complementary mechanisms and to optimized gene combinations in new cultivars. The third objective is to develop and apply phenotypic and genotypic selection technology for these traits to hard red or white winter wheat germplasm and cultivar development. This is an essential component of the technology transfer effort. Large-scale phenotypic screening data for Hessian fly and Karnal bunt resistance and genotypic marker data will be provided to cooperators.

3.Progress Report
More than 10,000 wheat breeding samples from 5 public breeding programs and 1 private breeding program were analyzed for molecular markers in the USDA-ARS Hard Winter Wheat Regional Genotyping Laboratory. All of the samples were screened with either simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers as requested by breeders and the data were sent to breeders in time for selection. We also analyzed two regional nurseries with 70 published markers linked to important traits of interest to breeders. The data have been sent to wheat researchers in the hard winter wheat (HWW) region.

We analyzed two biparental mapping populations and one association mapping population (420 lines) with a new 9000 SNP genotyping chip, and constructed two SSR/SNP maps with 2000 markers each. These markers will be further used to develop high-throughput SNP markers for traits of breeder’s interests. Meanwhile, we purchased a Sequenom SNP detection system and assembled a set of SNPs for some important agronomic traits for high-throughput analysis.

More than 3,200 wheat lines from 11 breeding programs and 4 regional nurseries or performance tests were screened for resistance to the Hessian fly. Approximately 4,125 lines were scored for resistance to wheat stripe rust in a screening nursery at Rossville, KS in 2010/2011. The nursery included three mapping populations, four regional nurseries or performance tests, and entries from nine wheat breeding programs. A stem rust screening nursery was also established at Manhattan, KS in 2010/2011 and differences in fungicide performance were determined.

Specific cooperative agreements have been established with six public wheat breeding programs to introgress resistance to Ug99 stem rust. Sources of single resistance genes in elite hard winter wheat backgrounds were provided to cooperators through material transfer agreements. The goal is to produce new varieties with two or more effective resistance genes through marker-assisted selection. Both backcrossing and forward breeding schemes are included.

In collaboration with Kansas State University researchers, experiments have been initiated to shorten the alien chromosome segment associated with wheat stem rust resistance gene Sr44. The purpose is to reduce linkage drag that reduces yield and quality of lines carrying the long version of the segment.

We assembled an association mapping population with 213 US hard and soft wheat breeding lines and cultivars. This population has been genotyped with 250 SSR markers and 9000 SNP markers. This population was evaluated for resistance to tan spot, soilborne mosaic virus, aluminum toxicity, powdery mildew, stripe rust and leaf rust in the field in 2011. Manuscripts have been completed for leaf rust and soil borne mosaic virus resistance.

In collaboration with researchers in the Triticeae-CAP project, we are conducting an association mapping study on heat tolerance in a panel of 167 spring wheat lines. Heat stress treatments are imposed after the flowering stage. Data collection includes chlorophyll content, grain yield per plant, and seed weight.

1. Development of genotyping-by-sequencing methods for crop plants. Rapid developments in DNA sequencing technology are quickly reducing the cost of sequencing in many species. To utilize this new technology in diverse crop species with large genomes, ARS researchers in Ithaca, NY, and Manhattan, KS, in collaboration with Cornell University researchers developed a simple procedure for making multiplex libraries for DNA sequencing. By multiplexing many samples the sequencing cost can be reduced to the point where it is practical for genetics and breeding. From these data, the researchers identified 200,000 molecular markers in maize and 25,000 molecular markers in barley at a relatively low cost per sample. This genotyping-by-sequencing method can rapidly produce hundreds of thousands of molecular markers in many diverse species, enabling new genetics studies in under-researched crops, novel germplasm, or thousands of samples in a plant breeding program.

2. Wheat germplasm releases with resistance to Ug99 stem rust. Researchers from ARS and Kansas State University in Manhattan, KS, discovered three new resistance genes effective against races of wheat stem rust, including the destructive new African race known as Ug99. These resistance genes were transferred to bread wheat from wild relatives of wheat including the species Aegilops searsii, Dasypyrum villosum, and Aegilops geniculata. These new genes will be useful in breeding resistance to the new races of stem rust.

3. New genes for resistance to Fusarium head blight of wheat. Fusarium head blight can significantly reduce grain yield and end-use quality of wheat. HYZ, a landrace of wheat from China, shows a high level of resistance to this head blight. ARS researchers in Manhattan, KS, in collaboration with Kansas State University identified four genes for head blight resistance in the landrace, with one gene showing a large effect on resistance. DNA markers closely linked to the gene were identified. Four other genes having smaller effect on resistance were also located. This Chinese landrace carries different resistance genes from those identified in another Chinese resistant cultivar, Sumai 3, and adds genetic diversity to the Asian Fusarium head blight resistance gene pool. These will be useful in creating new cultivars with improved resistance to FHB.

4. New high throughput marker for important resistance gene against Fusarium head blight of wheat. Fusarium head blight (FHB) is a destructive disease worldwide that significantly reduces both grain yield and quality of wheat. A gene (Fhb1) conferring resistance to the disease resides on the short arm of chromosome 3B. This gene has shown the largest effect on reducing FHB development. Several molecular markers for the gene have been developed and used in breeding programs, but they only give good results in certain groups of breeding materials. ARS researchers at Manhattan, KS, developed a new single nucleotide polymorphism (SNP) marker for Fhb1. This type of marker is suitable for high-throughput analysis and can reduce the cost and increase the speed of selection for resistance. The SNP marker will be useful for marker-assisted selection of Fhb1 in diverse wheat breeding programs.

5. Bacteria associated with Hessian fly may play a role in insect-plant interactions. The Hessian fly is an important insect pest of wheat. In this study, ARS researchers in Manhattan, KS, analyzed bacteria associated with Hessian fly at different developmental stages. Diverse bacteria were found in Hessian fly larvae, pupae, and adults. Most of the bacteria were transferred to the next generation through eggs. Removal of bacteria from the insect through antibiotic treatments resulted in high mortality of Hessian fly larvae, indicating that symbiotic bacteria were essential for the insect to survive on wheat seedlings. Similar bacteria were also found in Hessian fly-infested wheat, suggesting that Hessian fly larvae transmit bacteria into plant tissue, and that these transmitted bacteria may play a role in the wheat-Hessian fly interaction. This basic research may lead to novel approaches to controlling this insect.

6. Phytohormones may be important in plant defense against Hessian fly attack. Hessian fly is an important insect pest of wheat that causes damage to seedlings as well as lodging of adult plants. Salicylic acid and 12-oxo-phytodienoic acid were increased in both a resistant wheat variety and rice, which is a non-host. This suggests that phytohormones may be important components of the defense response. This research provides a foundation for future work on the role of phytohormones and fatty acids in the defense response against Hessian fly.

7. In the eye of the beholder: the effect of different raters on resistance gene mapping. Breeding for disease resistance has been a long-standing and important objective for plant breeders. Reflecting this, many studies have been conducted to find molecular markers that are linked to genes conferring disease resistance in order to assist breeding efforts through marker-assisted selection. These previous studies have been almost exclusively conducted using visual assessment of disease severity on the population of interest. Visual assessment of disease severity raises questions over the variability of ratings among different raters and how this affects the results and interpretations of these studies. Twenty-two individuals rated the same maize population for resistance to northern leaf blight, an important disease throughout the world. Differences between raters were significant and may affect results in some cases, but the genetic location of disease resistance genes was largely consistent.

8. Sequences of expressed genes of the wheat leaf rust fungus reveal many unique genes. The wheat leaf rust fungus is an economically important pathogen that causes significant losses each year. Researchers at ARS, Manhattan, KS, Agriculture and Agri-Food Canada, and university colleagues sequenced and characterized genes expressed in several life stages of leaf rust. Expressed sequence tags (ESTs) are DNA copies of messenger RNA transcribed in the tissue. ESTs represent a snapshot of what genes are expressed in that particular tissue, growth stage, and growth conditions. A database of 13,328 genes was made from almost 26,000 sequenced ESTs. The database was compared to DNA sequences from other related fungi, including wheat stem rust, wheat stripe rust, corn smut, and poplar leaf rust. Many genes are conserved between the five fungi, but over 40% of the genes from leaf rust did not match any sequences in the public database providing evidence that leaf rust has many genes that are species-specific. These unique genes may be important in host specificity or virulence.

9. Role of toxin sensitivity in resistance to tan spot of wheat. Tan spot is an important foliar disease of wheat that can significantly reduce wheat yields worldwide. Host-selective toxins produced by the fungus are thought to be responsible for leaf damage. ARS researchers and University collaborators in Manhattan, KS, evaluated 380 wheat accessions from different geographical origins for resistance to P. tritici-repentis race 1, the predominant race in the Great Plains of U.S.A. and western Canada, and for insensitivity to Ptr ToxA, a toxin produced by race 1. About 60% of accessions tested were resistant and only 24% were as susceptible as the susceptible check. A total of 230 accessions showed insensitivity to Ptr ToxA, but only 158 of them also showed resistance to race 1. The results suggest that insensitivity to Ptr ToxA is not the only factor for resistance to race 1, other factors such as Ptr ToxC might also contribute to tan spot damage in some accessions. The tan spot resistant accessions identified in this study should be useful sources for developing new tan spot resistant cultivars.

10. Genetic variation is low in Triticum mosaic virus. In 2006, a new virus was isolated in Western Kansas from the cultivar RonL. The virus was named Triticum mosaic virus (TriMV) and analysis showed that it was a very unique virus. The genome was sequenced, compared to other viruses, and no other virus is like TriMV in nucleotide or amino acid sequence. Since its discovery, TriMV has been found from Wyoming to Texas. ARS researchers and university colleagues sequenced the coat protein gene from fourteen TriMV isolates from Texas, Oklahoma, and Kansas. This study also looked at the coat protein gene of WSMV isolates within the same samples. Results showed that TriMV appears to be genetically very stable, while WSMV is very variable. These results may help in optimizing screening methods for resistance to these two viruses.

Review Publications
Khajuria, C., Buschman, L.L., Chen, M., Zurek, L., Zhu, K. 2011. Characterization of six antibacterial response genes from the European corn borer (Ostrinia nubilalis) larval gut and their expression in response to bacterial challenge. Journal of Insect Physiology. 57:345-355.

Bernardo, A., Ma, H., Zhang, D., Bai, G. 2011. Single nucleotide polymorphism in wheat chromosome region harboring Fhb1 for Fusarium head blight resistance. Molecular Breeding. DOI.10.1007/s11032-011-9565-Y.

Seifers, D.L., Martin, J.T., Fellers, J.P. 2011. Occurrence and yield effects of wheat infected with Triticum mosaic virus. Plant Disease. 95:183-188.

Li, T., Bai, G., Wu, S., Gu, S. 2011. Quantitative trait loci for resistance to Fusarium head blight in a Chinese wheat landrace Haiyanzhong. Theoretical and Applied Genetics. 122:1497-1502.

Yu, X., Bai, G., Luo, N., Cheng, Z., Liu, S., Liu, J., Warnke, S.E., Jiang, Y. 2011. Association of simple sequence repeat (SSR) markers with submergence tolerance in diverse population of perennial ryegrass. Plant Science. 180:391-398.

Li, X., Zhu, C.L., Lin, Z., Wu, Y., Zhang, D., Bai, G., Song, W., Ma, J., Muehlbauer, G.J., Scanlon, M.J., Zhang, M., Yu, J. 2011. Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundary. Molecular Biology and Evolution. DOI: 10.1093/molbev/msr011.

Fuentes-Bueno, I., Price, J., Rush, C., Seifers, D., Fellers, J.P. 2011. Triticum mosaic virus isolates in the southern Great Plains. Plant Disease. DOI: 10.1094/PDIS-04-11-0281.

Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler IV, E.S., Mitchell, S.E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 123:307-326.

Poland, J.A., Bradbury, P., Buckler IV, E.S., Nelson, R. 2011. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proceedings of the National Academy of Sciences. 108:6893-6898.

Xu, J., Fellers, J.P., Zhu, W., Joly, D., Eilam, T., Banks, T., Mayo, M., Ali, J., Mccallum, B., Saville, B., Linning, R., Dickenson, M., Antonov, I., Donaldson, M., Anikster, Y., Monro, S., Whnhoven, B., Moore, R., Borodovsky, M., Bakkeren, G. 2011. Gene discovery in EST sequences from the wheat leaf rust fungus puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi. Biomed Central (BMC) Genomics. 12:161.

Liu, Z., Bai, G., Zhang, D., Zhu, C., Xia, X., Cheng, R., Shi, Z. 2011. Genetic diversity and population structure of elite foxtail millet [Setaria italica (L.) P. Beauv.] germplasm in China. Crop Science. 51:1655-1663.

Poland, J.A., Nelson, R. 2011. In the eye of the beholder: The effect of rater variability and different rating scales on QTL mapping. Phytopathology. 101:290-298.

Noriel, A.J., Sun, X., Bockus, W., Bai, G. 2011. Resistance to tan spot and insensitivity to Ptr ToxA in wheat. Crop Science. 51:3:1059-1067.

Chen, M., Liu, X., Zhao, H., Stuart, J.J., Shukle, R.H., Yang, Z., Hulbert, S. 2010. Unconventional conservation among genes encoding small secreted salivary sland proteins from a gall midge. BMC Evolutionary Biology. 10:296.

Zhang, D., Bai, G., Zhu, C., Yu, J., Carver, B. 2010. Genetic Diversity, Population Structure and Linkage Disequilibrium in U.S. Elite Winter Wheat (Triticum Aestivum L.). The Plant Genome. 3:117-127.

Bockus, W.W., De Wolf, E., Gill, B., Fritz, A.K., Jardine, D.J., Stack, J., Bowden, R.L., Martin, J.T. 2011. Historical durability of resistance to wheat diseases in Kansas. Plant Management Network. DOI: 10.1094/PHP-2011-0802-01-RV.

Jayatilake, D.V., Bai, G., Dong, Y. 2011. A novel quantitative trait locus for Fusarium head blight resistance in chromosome 7A of wheat. Theoretical and Applied Genetics. 122:1189-1198.

Last Modified: 7/23/2014
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